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CIPRES Portal

The CIPRES Portal is currently under development. The portal is built on top of the CIPRES software libraries. The CIPRES project focuses on the inference of large trees. All software developed directly by the project is free and platform independent, but we are still working on a pain-free installation procedure. The portal lets you explore software that has been adapted to the CIPRES system without having to install it on your own machine. Calculations are carried out on the CIPRES cluster, at the San Diego Supercomputer Center.

Tools for Large Tree Inference (REC I DCM3 boosting is available for RAxML, and will be available for GARLI and PAUP soon).

Maximum Likelihood
GARLI

RAxML

Parsimony
PAUP
 
Bayesian
MrBayes (Coming Soon)  
Simultaneous estimation of
trees and alignments:
Poy (Coming Soon)
SATe (Coming Soon)

Note that each of the tree inference methods can be used as a standalone or in combination with a meta-heursitic to extend the range of problems that can be analyzed. The CIPRES portal is currently using Rec-I-DCM3 for RAxML, a divide-and-conquer technique as a higher level algorithm. For details refer to the discussion of Disk Covering Methods (pdf) and a specific discussion of Rec-I-DCM3 ( pdf). An implementation of the Nixon's ratchet (link to publisher) will be available soon.

Requirements:
Input: A matrix of DNA (All) or AA (PAUP,RAxML) sequences in NEXUS or PHYLIP format. A starting tree is not required, but you can improve upon an initial estimate of a tree. To do this, simply include this estimate in a Trees block in the NEXUS file. If there are multiple trees in the Trees block, the first one will be used.

Limitations:
At this moment, configuration of parameters by users is not supported, rather, default parameters are used, based on the recommendations of each program's author. Users can deploy up to 4 active jobs at any one time. Because the cluster is a shared resource, jobs that run over 72 hours are subject to being killed before they return results.

Output:
Output is returned to the user as a file in valid NEXUS format. A link to this file is displayed in the browser (HTML), and mailed to the user.
Results will be stored for 7 DAYS ONLY, then will be purged.

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